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Friday, May 31, 2013

I didn't read for pleasure much during graduate school, but then I had a baby. For awhile, as a new parent and a postdoc who would like to continue working in academia, there were not even thoughts about reading for pleasure. Funny enough, it's having a child that is starting to change this for me.

Even if there weren't a ton of evidence about the benefits of reading to children, I'd still do it, because I love the time I get to spend with my Little Bear, and the ways that we interact while reading. We've been reading to her since before she was born. But, as an infant, we mostly read her board books:

Then I had a brilliant idea. Sure, she likes pictures, and we still read her all sorts of wonderful books aimed at children, like, "Our Family Tree" (which is a simple, but not cringe-inducing introduction to evolution for kids):

But, she also likes to just listen to stories. Yes, Little Bear is only two (almost two and a half), so her vocabulary is still growing. That doesn't mean that she doesn't appreciate hearing all of the new words, and letting her imagination run wild a little bit. So, I figured that I would try reading a more grown-up book to her. I wasn't sure which one to choose, and then I met Brian Switek, and learned of his new book, "My Beloved Brontosaurus".

Slowly, the Little Bear and I have been working through this book, reading a little bit each night before bed. I have trouble pronouncing some of the dinosaur names, but she still gets the gist of the story, and it is ah-dorable when she really connects to a part of it. For example, tonight when I was reading a section about finding fossilized dinosaur eggs, with footprints of the baby dinosaurs she interrupted me to say:

"Oh, dinosaur eggs? (then her voice when up an octave) With teeny, tiny dinosaurs in them!"

Yes, sweet one, there were teeny, tiny dinosaurs. We've been really loving reading through the book together (it's also a great excuse for her to convince me to let her stay up just a little bit longer):

So, I have to pick on Brian just a little bit for ruffling my feathers with these tweets the other day:

I'm often asked if My Beloved Brontosaurus is a children's book. Nope, and not just because of the dinosex chapter. #brontotour
— Brian Switek (@Laelaps) May 22, 2013

My Beloved Brontosaurus is for adults who want to know why the dinosaurs they met as kids seem so different now #brontotour
— Brian Switek (@Laelaps) May 22, 2013

Yes, yes, I understand why the question and why the answers. My Beloved Brontosaurus is not a colorful, simply-worded children's book. As someone not very familiar with dinosaurs at all, I actually wouldn't have minded more pictures. My issue is that I don't think this book, or many similarly-styled books should be thought of as for adults only.

Parents let their young children watch all sorts of television shows, surf the internet, and play with all kinds of technology. Why, then, should we not expect that they might enjoy listening to a story that is above their reading level, but about something interesting?

Children are remarkably able to absorb and appreciate many things that we might not expect them to. I honestly didn't expect Little Bear to set through more than a page, and yet here we are, 31% of the way through the book. She scrutinizes the pictures that are included, but also listens intently to the text (and, maybe I'm a bit more liberal, but I actually didn't edit much out of the dinosex chapter). She may not remember it at all, or maybe she will. I think it is more important for her to hear all of the new words, to be challenged with unusual vocabulary, and to be entertained by her imagination.

As much as Little Bear loves to get the extra time staying up listening to "Brontosaurus", I am probably more excited to get to snuggle her, and to get to enjoy reading something for pure enjoyment.

Thursday, May 30, 2013

It would be generous to say that the brain trust is drained at Animal Planet (and that at most other television programs). For many science programs, it's all about ratings, and advertising funding. But, there are an awe-inspiring number of things about our Natural World that would make for excellent television. I'm calling on your to help crowd-source ideas for awesome (and real) topics for future television programming efforts. Off the top of my head (and in no particular order) I have listed topics and questions from myself and things friends have shared. I'll add more to the list if you post/email/tweet/fb/carrier pigeon it to me.

Thank you!
Melissa

Y'know what's better than a mockumentary? A documentary on anything below:

Wednesday, May 29, 2013

Three years ago I became a chimera. Again. I am also geneticist. Surprisingly, the two are unrelated.

One of my current research projects involves studying the genetic component of the autoimmune disease Rheumatoid Arthritis. In this disease, the body’s immune system attacks its own tissues, usually around the joints, causing moderate to severe pain, and breakdown of the nearby bone. Rheumatoid Arthritis affects approximately 1% of the population. But, for reasons that we do not yet understand, the symptoms go away during pregnancy, in about 50% of women (in other patients the symptoms stay the same or worsen). While conducting background research for this project, I came across an amazing feature of human pregnancy: microchimerism.

What does microchimerism mean? Let’s start with the biggest part of that word, chimera. In greek mythology, a chimera is a creature made of three different animals (a lion, a snake and a goat). In biology, the word chimera, or chimerism, can be used to refer to the existence of cells from genetically distinct individuals found in one person. So, microchimerism refers to the existence of a small set of cells of one genetic type intermixed with a large set of cells of another genetic type.

Let's think about development for a minute. My two year old shares about half of her DNA with her father, and about half with me. And, because we have raised her, she's picking up our habits, good and bad. She smiles like her daddy, loves sharing snacks with our dog, and furrows her brow to glare at me when she’s upset (exactly like a million pictures of me growing up). I do everything I can to keep her a safe, while still allowing her the freedom to explore her world. It turns out that I’ve been doing this since she was a tiny, unrecognizable embryo.

Okay, you had a baby, but how did you become a chimera?When I was pregnant, my body provided nourishment and protection. A portion of that protection came in the form of my immune system providing defense against infections. During pregnancy, some of my immune cells actually passed through the placenta, and became incorporated into my daughter’s developing body. This means that although most of the human cells in her body are her own (a unique combination of DNA from her father and from me), incredibly, there are some cells in her body that are actually mine. Even more extraordinary is that this sharing of immune cells is a two-way street. Some of the immune cells from her growing body passed back into mine. A subset of these cells became incorporated into my body, and will continue to replicate, sometimes for decades (Gammill and Nelson have a great review here, if you want to learn more).

Immune cells cross the plancetal boundary and
become incorporated among genetically dissimilar
cells where they continue to replicate

Whoa. So, you are both chimeras?
Yes. In fact, this exchange of cells occurs during all human pregnancies, with both male and female embryos. This means that some women have a small number of cells with male DNA from their sons, and men have some cells with female DNA from their mothers. So, we are all born as chimeras. Scientists are just now starting to understand how this exchange of cells affects our biology. My current interest in this topic is that fetal microchimerism might be responsible for some of the alleviation of symptoms during pregnancy for patients with Rheumatoid Arthritis.

It is also just mind-blowingly awesome.

It amazes me to realize that, right now, some of my daughter’s cells are incorporated into my body. There is, literally, a physical part of her with me wherever I go. And, similarly, a few of my cells are incorporated into her. The scientist in me is awestruck. But, as any parent will tell you, it doesn't change how I feel. Regardless of our genetic relationship, I will always be a part of my daughter, and she will be a part of me.

I loved all of the dances, and became curious about research into the health benefits of dancing. In looking up research about dancing, I came across a very curious article, indeed, published in BMC Public Health.

Sure, the title seems like a question that should be investigated. And I was happy that the article is Open Access so that I could read all of the paper. When I first started reading, I thought that maybe someone had accidentally used the wrong tense. Then, as I continued to read, I realized that no, they had not. The entire paper discusses what "will" be done. I had originally glanced over the word "protocol" in the title, but reading the article made it abundantly clear: this entire paper is a written protocol for a study that will be done (or, as the manuscript states, is now underway).

How curious.

I'm not entirely sure what to think about it. Definitely protocols should be published, but I tend to think of protocols being published alongside the analysis of the results so that one can judge whether the protocol was successful or not (or somewhere in between). In addition, I think that companies should publish protocols for technologies and services that they are offering. I certainly like the idea of studies publishing very detailed protocols, but this paper reads like a grant proposal. And a grant proposal without any data, at that. As such, reading this paper ends up being disappointing (because I really wanted to learn about whether social dancing can prevent falls in older adults!), and, well, perplexing. I am not sure what value this kind of paper serves in a peer-reviewed journal. Even new methods and protocols are published with some sort of assessment of their utility. I think that sharing this protocol is useful, but not in a journal format, or at least not until it has some data to report.

Are there fields where publishing protocols in peer reviewed journals, prior to data collection, is standard procedure?

He is a prolific science writer (over 111 articles written last year), travels (although not as often as he'd like due to reduced funding for journalists), and is particularly interested in writing about evolution and climate change. We talked about increasing communication between scientists and journalists. He gave me some great examples of how journals can best get their content to journalists, and we discussed how Scientific Societies can facilitate interactions between science writers and researchers. I'm hoping to make some summaries of his suggestions and then look into how the Societies I am a part of (SMBE, SSE, and ASHG) all do these, and how we can do them better.

In addition to figuring out how to connect scientists with journalists, it might be useful to know what to say once we're actually connected. Ed Yong has put together a great set of tips for researchers to keep in mind when talking to journalists.

Thinking about science writers, there is a big difference between previous approaches to writing and current approaches that David was quick to hone in on during lunch. Although his articles are posted electronically, he started writing before the internet, and when writing he still keeps in mind the regulations for writing a newspaper article, specifically length restrictions. As newspapers move to more and more online content, there are less concerns about length restrictions, but, the ability to post longer content may not always translate into longer articles. Why? Because they won't be read.

David lamented the short attention span of today's information consumers. He is completely right. I am guilty of it, and guilty of feeding into it. I like to get the gist of an article quickly, I love the tidbits, and I also expect my readers will want something they can comprehend and digest in the few precious minutes they'll spend on my blog. I still appreciate in-depth articles, I am just limited in the number of them that I can, or do, process a day. That does not mean that longer articles will disappear. For example, see this long, excellent article about a rare bone disorder by Carl Zimmer.

Okay, so there will, at a minimum, be quite a lot of variation in length of electronic-only articles. There are other advantages to writing in an all-electronic format, over for print, including the ease of sharing articles, and the ability to include multiple and colorful graphics. Another advantage of newspapers moving to electronic publishing, suggested by Ed Frenkel at lunch, is the ability to invite guest posts from scientific experts. Scientists are busy with their own research, and cannot write full-time, but many of us like to contribute to the public discussion, and may be able to do so as guest posts.

I am certainly limited in the amount time that I spend writing
and researching for posts because I do this after my day (and night)
job of being a researcher. But I feel a drive to communicate with the public about science. I am always excited to talk about science, but I especially love hearing the questions that start pouring out. Successfully communicating science involves providing enough background to lead to understanding, and to spark imaginations. Science lets each of us tap into the wonder we often left in childhood. It is the responsibility of scientists - at the minimum those that are supported by federal funds - to engage the public. I truly believe that funding agencies and universities are moving (perhaps at a glacial pace) to encourage more interactions with the public, but it seems that the academic machine still does not properly weight the value of scientific outreach (although I have heard glacial paces are increasing).

Science writing is one way to engage the public. Being open and cooperative with journalists is another. And there are many others (visiting classrooms, volunteering at museums, hosting students, mentoring, meeting with politicians, and on and on).

David inspired me with his enthusiasm for communication, his wit, his passion for science, and his instant likability. There was one other thing about him that surprised me: David Perlman is 94 years old.

Thursday, May 23, 2013

We are excited to be hosting the 8th meeting of the Bay Area Population Genomics group at UCSF Mission Bay on June 8th! Thanks to support from Ancestry.com and the Institute for Quantitative Biosciences (QB3 @ UCSF), this conference will include breakfast and lunch. In addition, we will also have a reception during the poster session, so we highly encourage you to preview your work at BAPG before heading out to summer conferences.

Please register at http://tinyurl.com/a8h6uo8, and sign up to give a talk or poster. Registration is again free, but required by June 3rd.

There is paid parking in the lot/garage at the corner of 4th and 16th streets, and we have a limited number of parking passes for people that sign up to present and/or make a strong effort to carpool (please email me for details).

We are very much looking forward to seeing you at UCSF in a few weeks!

Best,

Ryan

This is an excellent opportunity to share ideas, learn about new topics, and meet other researchers! Unfortunately, this is the same weekend as the Miller Symposium that I've been co-organizing (I just finished up my informal presentation for it), but I encourage you all to participate.

Tuesday, May 21, 2013

In mid-April I got the official decision that my K99 application would not be funded. There is a lot of competition for funding, so I wasn't completely surprised, but I did want to know:
1. What were the concerns/criticisms of the application?
2. Based on the reviews, is it worth resubmitting?

It took a frustrating couple of weeks before I got the comments on my application (but glad to have them). I immediately contacted the Program Officer and set up a time to discuss the comments.

I have to say that I was pleasantly surprised with the comments from the four reviewers, especially given the rejection. Many of the reviewers listed both the Strengths and Weaknesses of my application. Let me tell you, reading the "Strengths" were such a boost, and provided me so much motivation to resubmit (and work on my other projects) that it really helped me read the "Weaknesses" sections critically.

As a postdoc, I often feel a lot of pressure from established professors, from my peers who are applying for jobs, and from collaborators, to research, research, research, and, more importantly, to publish, publish, publish. I am advised to work, and to focus, and to always be on game because of how intensely competitive it is in the job market. I have been advised that I will interview well (yay!), but will have a more difficult time securing interviews because my publication record is weaker than my peers (boo). Yes, this is all true. I very much value having realistic expectations, and appreciate the motivation to do my best. But, a part of me feels frustrated that the focus seems to be on doing my best to secure a job, instead of doing my best because it is the right thing to do.

Ironically, it was reading the notes from my rejected K99 application that I have found the most positive motivation. If you'll oblige me, some tidbits from the "Strengths" sections:

"The candidate has a strong background and publication records in
computer genetic data analysis. She has a clear career goal and career
development plan."

Oh, well, thank you very much!

Okay, so what are the weaknesses? I'm ready. Hit me with it:

"Aim 4 is experimental and no training for this seems to be evident."

"Since her research in the independent stage will involve collecting and analyzing biological samples, there is a need for training plan in biology research."

There were also some more specific criticisms, that, after carefully reading them, came about because I did not provide enough detail.

Overall:
From my reading of the criticisms, I think that my application had some flaws that can be readily addressed in a resubmission. I am an evolutionary biologist. I have done some experimental work, but did not highlight that in my application (though not with humans, as a propose here). Three of four aims were computational, and I proposed a rather ambitious fourth aim that was meant to be a collaborative computational-experimental aim. I did not highlight how much I expected this aim to be collaborative, and, given my limited experience in running wet-lab experiments, there were some criticisms of this aim that could be addressed with an appropriate mentor.

So, the big question is: Do I find a mentor who is an expert in experimental biology, in addition to gaining training in statistical genetics, OR, do I alter the fourth aim (which is supposed to be during my independent stage) to be more computational?

That's where talking to the Program Officer comes in.

This morning (7am PST) I spoke with the Michelle Hammlet, the Program Officer for the Institute where my application was reviewed (National Institute of General Medical Sciences). She was fantastic! We discussed the criticisms, how best to address them, and although she was understandably non-committal in what the "best" course of action for me will be, she was happy to discuss alternative options. Some things that I found particularly useful from our conversation. It may seem obvious after the fact, but while working on the application, I found myself getting bogged down in details, so taking a step back really helped:

- Be clear to differentiate between the K99 and R00 phases - taking care to make sure that I obtain all the training I need during the K99 phase to proceed to the R00 phase independently.
- The proportions of the application dedicated to the training (K99) and independent (R00) phases need not be equal. Depending on how much training is needed to reach the candidate's goals, some applications may have 25% devoted to the K99, while others may have 50% or more devoted to the training plan. Try to focus on the details of what kind of training I need to be successful in the R00 phase, as that is the focus of this application.
- A proposal that is all computational will still be competitive. This one really struck me, because I've been told from many PI's that I need to have an experimental component to my independent research.

So, the answers to my initial questions are:
1. What were the concerns/criticisms of the application?
I propose an aim that is broadly experimental without providing a training or collaboration plan.

2. Based on the reviews, is it worth resubmitting?
Yes! But, exactly how to frame the resubmission is not yet clear.

"My question is what if evolution went a different way and instead of
going back into the sea, from which they came originally, they went into
the air and we evolved a nature that could fly instead of swim. "

I love the creativity, and admire all of the skill that went into creating it. Like all of her artwork, it makes me a little uncomfortable. But that seems to be her shtick. Generally science fiction is very limited in its imagination of non-human aliens (they all basically look just like humans with a different skin pigmentation or frills on their faces). The Skywhale is... a creature of its own. It is not simply a whale with wings.

But, I also have a hard time thinking about the Skywhale in evolutionary terms (although I do love that she used that as inspiration). Just off the top of my head, I wonder:
- How much lift would something so large need to get off, and stay off the ground?
- What about its skin? The whale evolved for aquatic life - how would it have transitioned to air life while still maintaining similar skin? It would also likely need to have darker pigmentation, or some sort of skin covering (fur? hair?) to prevent skin damage from being out in the direct sun all the time.
- Would it need to lose the blubber because, on land or in the air, it wouldn't need to stay as warm as in the depths of the ocean.
- Why does it have 10 teats? I have nothing against breasts, but 10 doesn't make a lot of sense. A rough rule of thumb is that mammals have twice as many teats as they (usually) have offspring. But also, larger mammals have fewer offspring. So, I would expect the huge Skywhale to have one baby, and two teats.
- And why does it still look like a whale at all. This looks like a whale (that evolved to live in the ocean) suddenly changed to live in the sky. Such a transition would like take millions and millions of years, and it seems very unlikely that its face would still resemble a whale at all.

But, being inspired by science, and conforming to science are two different things.

Friday, May 17, 2013

As a member of the
Society for Molecular Biology and Evolution, I
am writing to request that the Society Council and Editors of its
journals please consider moving quickly to adopt a preprint-friendly
policy at MBE and GBE.

I joined the Society for
Molecular Biology and Evolution in 2007, just before attending my first
SMBE meeting. It was fantastic! A group of grad students piled in a van
and took turns driving the 17 hours through beautiful landscapes to
beautiful Halifax, Nova Scotia. I remember being completely overwhelmed
with the quality and quantity of science presented at the meeting.

Since
then I have attended most SMBE meetings, co-organized a symposium, helped to publicize those
meetings and presentations, and am very excited to have recently
published a paper in Molecular Biology and Evolution.
I have always been impressed with the the activities of the Society, and
plan to continue being an active member throughout my scientific
career.

However, as a new investigator, and one who has already submitted to the arXiv, I was surprised to hear, from various
sources, that neither MBE nor GBE will consider publishing papers that
have been submitted to the arXiv. I thought that surely this cannot be
true. Following good scientific procedure, I decided to investigate for
myself, going to the source (since nothing regarding prepints currently
exists online at the MBE or GBE websites). Yesterday I received this
very kind response from Elizabeth Raffaele (emphasis mine):

Dear Melissa

I had to check this out with the Editor in Chief as I want sure of the answer.

He has advised that current policy at both MBE and GBE prohibits arXiv distribution prior to publication.
New arXiv-friendly policies are under consideration and will be
implemented in the near future. So, authors should take a conservative
approach for now, and not post it on arXiv.

I hope this is helpful.

Best wishes
Elizabeth

I
very much appreciate the prompt and careful response (many thanks to
Elizabeth). But, as a Society member, and someone who highly values the
research published in MBE and GBE, I am completely disappointed with it.

The arXiv is a
pre-print server that allows scientists to connect
with their peers, share information, and gain critical feedback on
manuscripts. I have found that submitting papers to the arXiv is a
fantastic way to increase interest in research, share current results,
and promote discussion. However, the arXiv is not a peer-reviewed
resource. Unlike mathematics and physics, where often the arXiv is the
final submission for papers, in Biology, I think the benefits of peer
review are unparalleled. The arXiv does not replace peer review. The
editors and volunteer reviewers of MBE and GBE provide an invaluable
service to the scientific community. I am proud to be part of a Society
whose journals are known for publishing high quality research. I can
think of no reason that
preprints should be excluded from consideration for publication at MBE
and GBE. If
anything, preprints will allow extra scrutiny, and extra advertisement,
for articles that pass peer-review, and are published in MBE or GBE.

I hope that you will please consider the benefits of
allowing submissions to MBE and GBE of articles that have also been
uploaded to preprint servers.

Thank you very much for considering this request.

Sincerely,
Melissa

--
Melissa A. Wilson Sayres, PhD
Miller Fellow

University of California, Berkeley

________________________
I just got an update @11:42AM that it is on the Agenda to be discussed at the SMBE Meeting in Chicago. I am very excited (nervous?) to see what is decided.

Thursday, May 16, 2013

Angelina Jolie wrote about her decision to have a double mastectomy after learning that she carries a version of the BRCA1 gene with mutations that are significantly associated with developing breast cancer, speaking with her doctor, and considering the risks and benefits to herself, and for her family.

By ILA-boy

Many people have reacted, but I particularly like this response from Judith Soal that introduces the complexity of understanding the genetic component of diseases. We still have quite a lot to learn about the relationship between genes, environment, and disease, but we do know that some genetic mutations increase susceptibility to disease, but also that people without known genetic mutants are often affected by diseases due to environment, to novel mutations, or, by chance. Moreover, rarely is the culprit of a disease a single gene. But, for now, we'll leave this to others.

I want to focus on something else. Something that is relevant to every person. Something that both of these articles touch on. Let me highlight them for you.

From Jolie's article:

"The cost of testing for BRCA1 and BRCA2, at more than $3,000 in the United States, remains an obstacle for many women."

From Soal's article:

"Fortunately I live in the UK, where the NHS offers free genetic screening..."

Both of these articles mention the cost of the genetic screening. In the United Kingdom, this cost is covered, while in the United States, it is quite expensive, at least for health insurance plans in place prior to the passing of the Healthcare Law. But even if covered by insurance, someone is paying a lot of money for this testing.

Owns?
Yes, they own it. Myriad holds a patent on the sequence of those genes. This means, even if you wanted to sequence your own BRCA1 and/or BRCA2 genes, you would have to pay a fee ($3,000-$4,000 to Myriad) because Myriad owns the right to know the sequence of every human BRCA1 and BRCA2 gene. All 7.1 Billion people (yes, we all have chromosome 17 an chromosome 13, and regardless of the genetic component are all susceptible to breast cancer, as well as many other associated cancers). This patent is currently being disputed in the Supreme Court.

If it's a patent, what did they develop?
Myriad did not develop the BRCA1 or BRCA2 genes. Myriad did not create the mutations in BRCA1 or BRCA2 that are associated with breast, or other cancers. Myriad has no right to prevent anyone from knowing what the sequence of our genes are.

This patent gives Myriad ownership of information about my body that has always been a part of me. is akin to giving them the right to know (and to tell me, or not) what color my eyes are, even though I could use a mirror to figure it out. Using the mirror (doing it myself), would violate the patent unless I paid Myriad money. It is like allowing Myrad to to charge me thousands of dollars to know what my blood type is (even though I can order a couple, super-nifty, blood-typing cards for twenty bucks ).

Sure, Myriad can offer their test (which uses technology that is no different than thousands of labs around the world use daily). But, they have no right to prevent other people, or companies, or ourselves, from conducting tests to answer the same questions. Questions about ourselves.

Wednesday, May 15, 2013

About a month ago I blogged about some awesome pants designed and made by Holly Renee in Berkeley (here). Well, we got in touch, and now, not only do I have DNA pants, but she made a teeny matching pair for the Little Bear!

They are comfortable, and nerdtastic.

Regular and pint-sized DNA pants!!!!

If you'd like to find me at SMBE13 in Chicago this summer, I'll be the one wearing awesome.

Bladder traps on the roots of the "common bladderwort" (Utricularia vulgaris), by pellaea.

The genome of this plant is so interesting because it is quite small. The authors go so far as to call it a "minimal" genome.

What makes it minimal?
Often, when talking about genetics, we usually talk about the genes. These are the pieces of DNA that code for proteins. These are "coding" regions. There are also pieces of DNA that do not code for proteins. We call these "non-coding". The genome is the full set of coding and non-coding DNA. Some species have lots of non-coding DNA (like humans, and onions). Other species have very little non-coding DNA, including this bladderwort.

Although the bladderwort has nearly 10,000 more genes than a human, these genes are very compressed and overlapping so that the bladderwort genome and the human genome have about the same amount of coding DNA sites. But, the bladderwort genome has a lot less non-coding DNA, for a total genome size of 87 million bases, while the human genome has bloated amount of non-coding DNA a total genome size of 3,164.7 million bases. That's over 36 times more total DNA than the bladderwort! (Note: the total DNA content does not indicate complexity - whatever that is. Check out the range in genome size of "flowering plants" at the top of this plot.)

Was the bladderwort genome always so slim?
No. By comparing with other yummy plant genomes (papaya, grape, tomato and Arabidopsis, a flowering mustard weed), and by analyzing the gene content within the bladderwort genome, Ibarra-Laclette et al. concluded that the bladderwort genome, like many plants, experienced duplications of its whole genome. Afterward there were some losses of large regions of DNA, but much of the reduction in DNA content from these duplications occured through what they call "microdeletions", where small pieces of DNA here and there were deleted.

Are all bladderworts the same?
Just like there are many species in the taxonomic family Hominidae (orangutans, gorillas, bonobos, chimpanzees and humans), there are many species in the the taxonomic family of bladderworts (called Lentibulariaceae). Genome shrinking is not unique to this species of bladderwort, but is also not shared across all species of bladderworts. Curiously, genome size in the whole family of bladderworts varies from 60 million base pairs to 1,500 million base pairs. That is a lot of variation considering that genome sizes across all Hominidae are all within the range of 3,000 million base pairs (plants genomes get no respect).

Although genome size varies quite a bit, the bladderworts look and function in similar ways. So, while some of the noncoding sequence is functional (providing instructions for how and when to turn the genes on and off, in time, in response to the environment, and in particular tissues), it seems highly unlikely that there would be so many more instructions in the bladderwort with 1,500 million base pairs than in the bladderwort with 60 million base pairs. A lot of the non-coding DNA, therefore, is likely also non-functional.

bladderwort (Utricularia vulgaris) in the water. by H. Zell.

In the closing line of the bladderwort genome paper:

In summary, U. gibba genome architecture demonstrates that angiosperms can evolve diverse gene landscapes while overall genome size contracts, not only during expansions. Furthermore, in contrast to recent publications that highlight a crucial functional role of non-coding DNA in complex organisms such as animals24, the necessary genomic context required to make a flowering plant may not require substantial hidden regulators in the non-coding ‘dark matter’ of the genome.

Friday, May 10, 2013

I was inspired to look up balance on bicycles after we bought into the "balance bike" trend, and it actually worked! Here's a video (ignore my excited yelling at the end) of our two year old balancing on her teeny-tiny bicycle. I never expected that she would pick it up so quickly.

I guess, when I think about it, there are two main aspects to learning how to ride a bicycle:

1. Pedaling

2. Balancing

I learned by pedaling first, then, when I was older, learning how to balance (and falling quite a bit). Now that I've seen it in reverse, I'm amazed. Of course, balancing is probably easier to learn when your center of gravity is closer to the ground. It also may be easier to learn to balance on a bicycle when you are still learning about balance when walking.

Here's a summary of some research I found from UC Davis, studying balance on bicycles:

Thursday, May 9, 2013

I was going to update a previous post about sperm stem cell transplants in boars, when I came across a very recent paper with a similar technique in the Rhesus monkey, and I couldn't pass it up. So a little of the background content here is duplicated from that previous post.

Sperm cells are the vesicles used by male mammals to pass on their DNA to their offspring

Human sperm cells, Wikimedia Commons

Sperm are made from sperm stem cells. Each healthy cell in our body has a finite life, so we need stem cells (adult stem cells) to make more cells when the old one dies. There are
many kinds of adult stem cells that can only make more of a certain kind
of tissue. For example, there are skin stem cells to make more skin cells, there are
blood stem cells to make more blood cells, and there are sperm stem cells to make
more sperm cells. For the paper I'm talking about today by, it is the sperm stem
cells that are important.

Hermann et al. worked with male rhesus monkeys that had undergone chemotherapy, which can permanently damage fertility.

They took healthy
sperm stem cells from donor monkeys, and implanted them into the testes of chemotherapy-treated recipient monkeys. It is important that they transplanted sperm stem cells, which will keep replicating and making new sperm throughout the recipient monkey's life, versus just sperm cells, which will die and not continue to replicate. This transplant wasn't 100% successful, but in over half of the cases, there was evidence that the donor sperm stem cells were, in fact, replicating and producing sperm. Further, the researchers were able to confirm that donor-derived sperm could fertilize an egg (although, curiously, of the sample of sperm from the chemotherapy-treated monkey, only about 9% of the fertilized eggs were genetically similar to the donor, suggesting that not all spermatogenic function was lost during the chemotherapy treatment).In the boar study, the scientists were looking to add functional sperm, where none (or very, very few) had previously existed, meaning that nearly all of the sperm generated would be from the donor. This would mean that if applied to genetically infertile XY-individual, that person's offspring would be more genetically similar to the donor, than to the transplant recipient.However, this study allows for a different approach, and application in humans. Considering the case when a sperm-making individual knows that they will be undergoing a procedure (such as chemotherapy) that affects their ability to make functional sperm. That person could, in theory, have some of their own sperm stem cells extracted, then transplanted back after the fertility-affecting procedure was completed. Wow.

Wednesday, May 8, 2013

I strive to be scientifically accurate as often as possible in all aspects of my life. That also extends to how I explain the world to my two year old.

I'm very excited about a book I just learned about called,"It's NOT the Stork". This book goes through basic vocabulary for body parts, introduces "where babies come from", and even highlights how to stand up for yourself, all in simple terminology. I'll add my own thoughts at the end, but I agree with everything this reviewer said (well, except that I'm not an RN):

When my kids started asking reproduction and anatomy questions, I checked out and read the reviews of every book on the subject I could find. I'm an RN, so it was important to me that it was accurate as well as engaging for my kids. I am so glad I picked this one. My children were 4 and 6 when we bought this book, and they absolutely loved it from the first reading. So did I. It has all the information I was hoping for and it is presented so appropriately for the age. Nothing is scary or more detailed than necessary. The illustrations are bright and fun and keep the kids engaged. The book is set up in such a way that is easy to navigate - that is, you can read it from beginning to end, and it flows appropriately - starting with body parts and boy/girl differences, reproduction in the middle, and a small section at the end about good and bad touches. You can also easily jump to the section that you or your child prefers without taking away from the book. For example, my daughter is fascinated by the cartoon showing the sperm swimming to the egg and we often just start there.

As a parent of young children and as an RN, I recommend this book to all parents.

My dad's parents were a doctor and nurse, and my family was always very practical about explaining anatomy. Penis, scrotum, vagina, vulva, and anus, are not bad words. They are medically accurate vocabulary. Vocabulary that I learned from a very young age. I'm so proud of my parents (and grandparents) for having the good sense to teach us what was correct, and to not be embarrassed by medical terminology. I hope to be as good with my daughter. Although she is two, I see no reason why we cannot learn all of the body parts. Why should she only learn, "head, shoulders, knees, and toes"? We don't dwell on any particular anatomy, and there is no need to make a big deal about it. However, it can be immensely useful for her to understand what all the parts of her body are, and what they do. This particular book is, in my opinion, still a little out of her age range, but I'm glad to have it as a reference for when we do need it (the cover recommends 4 years old).

I think we do a disservice to our children if we don't expect them to act maturely about their bodies. But then, how are they supposed to act maturely if we don't set that example?

Tuesday, May 7, 2013

There are over 1600 articles in the Second Edition of Brenner's Encyclopedia of Genetics, and exactly one of them is written by yours truly.

I wrote the entry for the Pseudoautosomal Linkage Region (which I would have preferred to call the Pseudoautosomal Region). Unfortunately the new website only has a few previews right now, which I wasn't able to access, but you might be able to get an idea of the content by looking at the previous collection. I am hoping the electronic version will be up and active soon - I'll post here when it is.

You can always purchase the hardbound copy for the low, low price of... oh, uh, nevermind. You should probably just wait until the website becomes active, or convince your school's library to buy it.

Every day I enjoy watching the interactions between Little Brown Dog and Little Bear. They are forever friends, and, I am amazed at how much patience our 10lb shelter dog has with this inquisitive toddler.

Things we've said to Little Bear, in reference to Little Brown Dog:

"He doesn't understand that you're just trying to brush his fur with that wrench." (We do let her brush his fur sometimes with a little brush, but now she wants to do it all the time.)

"Please do not 'fix' his face with your screw driver." (She's been 'fixing' ouchies, very gently using a screwdriver, like a, a... I'm not really sure. Actually, it is kind of like a tricorder from Star Trek that she waves over the "ouchies", but Little Brown Dog doesn't know that. He's more of a Star Wars fan.)

In humans, genetic females have two X chromosomes and genetic males have one X chromosome and one Y chromosome:

You might have noticed from the cartoon above that the human Y is much smaller than the human X. But, it wasn't always this way. Ancestrally, the human X and Y were the same size, and had the same genes. Over time, however, the Y has shrunk, but both the X and Y have also gained some genes. To better understand how the X and Y became so different, and how the evolution of the two sex chromosomes are correlated, we asked three main questions:

1. What has been lost from the Y?
To know which genes were lost, we first had to identify which genes were on the ancestral sex chromosome pair. By comparing the genes on the human X with the genes the X in other species, we identified a set of genes that were likely on the ancestral X chromosome: 600 in total. Then, by searching the Y chromosome for the relics of all of these genes, we identified three classes of sex-linked genes. We should think of each of the 600 ancestral genes as a pair (with one copy on the X, and
one on the Y). All of these pairs have a working copy on the human X. Some pairs have
a working (functional) copy on the Y, some have a broken copy on the Y
(degraded), and some are missing their Y-copy.

Many genes have been lost from the ancestral Y, but a few persist.

So, while some Y-linked genes have survived (I have another paper discussing this), and there have been some unique additions to the Y chromosome, we can see that the Y has lost functional capabilities for 96.83% of the genes that it once shared with the X. Wow!

2. Are there indicators of whether a Y-linked gene will be retained?
We can learn about the evolution of the sex chromosomes by studying differences between classes of sex-linked genes defined above. Specifically we asked, do features of X-linked genes suggest whether their Y-linked partner are retained or lost? In some cases, yes, they do.

First, we found that human X-linked genes with very few changes across mammals were more likely to have a working Y copy. So, if a gene is important enough to survive over long evolutionary time
in roughly the same condition across very different species, then it might be very useful to the organism, so it would be important to have that gene in a working form in both males and females in the same species (human).

Second, we looked at expression. Genes can sometimes be "on" (which we would call expressed) or "off" (not expressed), but more often they can fall within a range. It's like a light with a dimmer switch. The light can be turned on very brightly, but can also dimmed to a very low level without being "off". We found that X-linked genes that were highly expressed (bright) were more likely to have a working Y copy. This might mean that, for these genes, the level of "brightness" or expression is important, so that it is highly beneficial for these genes to be working very hard in both females and in males.

3. Does gene loss on the Y affect the evolution the X?

Okay, so some features of the X-linked partner might predict whether it's Y-linked partner will survive, but is there any feedback from the Y back to the X chromosome? Yes!

Let's think back to that first picture: females have two "big" X chromosomes, while males have one "big" X and one "little" Y. And, I've shown you that the Y chromosome has lost (either because of broken copies, or completely lost) almost 97% of the genes that it once shared with the X. This might lead you to believe that there are more genes expressed in females than in males. But, in many mammals, females silence most of the genes on one of their X chromosomes (X-inactivation), to equalize the dosage of genes expressed between males and females.

Although it has been hypothesized, we showed that the pattern of genes subject to silencing in females among the three classes above is consistent with a process whereby silencing evolves in response to gene loss on the Y chromosome. Moreover, this pattern suggests that some amount of time must pass to allow the signal (that the Y-linked partner is no longer working) to reach the X-chromosome before silencing can occur.

The paper is open access, so if you are curious, you can read it here.

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